Well I’m not sure if its a problem, I’m trying to get a better understanding of how Sage and the deployment process should work.
It looks like they are only using Sage 10, not using Bedrock or Trellis.
We are using Kinsta, so I went into each website’s server that is live and looked at the theme folder and each site has the complete folder structure of the git repo (everything that you would see when your building it locally for the firs time). They don’t have the repo connected to the server in anyway, so it looks like when the developer went to push a site live for the first time, he just manually copied everything from his local environment over to the server and than installed yarn & node on the server, then ran the build script.
So right now if I wanted to work on a live site in a local environment, I would have to clone the repo, then either use like a migration plugin like Duplicator to copy over the WP Database & plugins, etc., from the live site. Use a tool like Local by FlyWheel to run WP locally, run the migration tool locally and whatever else to get it up locally. Then when im done editing it and I run the build script, I could either copy over the changed files like you said or do what he did and probably just dragged the whole folder over to the server.
Or like I said earlier, since he has yarn/node installed on the server I can just SFTP to the server, edit the files and run the build right there on the server BUT when I was told that’s how they have been doing it, it just didn’t seem right. Which leads me to believe that the developer either didn’t fully know what he was doing or just didn’t care.